**R语言生信GO分析报错**
在进行生信分析中的Go分析时,按照教程运行脚本06中goplot(ego_BP)画有向无环图时,如下为视频教程截图
自己运行时反复报错
请教多方无果,网上查找资料仍无果,恳求指点。原脚本运行包俯下。本人使用R版本为4.4.1
rm(list = ls())
load(file = 'step4output.Rdata')
library(clusterProfiler)
library(ggthemes)
library(org.Hs.eg.db)
library(dplyr)
library(ggplot2)
library(stringr)
library(enrichplot)
# 1.GO 富集分析----(用差异基因做富集分析)
#(1)输入数据:上调和下调基因的ENTREZID
gene_up = deg$ENTREZID[deg$change == 'up']
gene_down = deg$ENTREZID[deg$change == 'down']
gene_diff = c(gene_up,gene_down)
#(2)富集——运用函数enrichGO()
#以下步骤耗时很长,设置了存在即跳过
f = paste0(gse_number,"_GO.Rdata")
if(!file.exists(f)){
ego <- enrichGO(gene = gene_diff,
OrgDb= org.Hs.eg.db,#分析基因的类别:人类?鼠?
ont = "ALL",
readable = TRUE)#"readable"让基因名称变得可读
ego_BP <- enrichGO(gene = gene_diff,
OrgDb= org.Hs.eg.db,
ont = "BP",
readable = TRUE)
#ont参数:One of "BP"(生物学过程), "MF"(分子功能), and "CC"(细胞组件) subontologies, or "ALL" for all three.
save(ego,ego_BP,file = f)
}
load(f)
#(3)可视化
#条形图
barplot(ego)
#分面条形图
barplot(ego, split = "ONTOLOGY", font.size = 10,
showCategory = 5) +
facet_grid(ONTOLOGY ~ ., space = "free_y",scales = "free_y")
#气泡图
dotplot(ego)
#分面气泡图
dotplot(ego, split = "ONTOLOGY", font.size = 10,
showCategory = 5) +
facet_grid(ONTOLOGY ~ ., space = "free_y",scales = "free_y")
#(3)展示top通路的共同基因(即P值比较小的基因),要放大看。
#gl 用于设置下图的颜色
gl = deg$logFC
names(gl)=deg$ENTREZID
#Gene-Concept Network,要放大看
cnetplot(ego,
#layout = "star",
color.params = list(foldChange = gl),
showCategory = 3)
goplot(ego_BP)
输入以下命令:
vim /etc/ssh/sshd_config
在此文件中找到以下配置项:
#ClientAliveInterval 0
#ClientAliveCountMax 3
去掉注释,改成
ClientAliveInterval 30
ClientAliveCountMax 86400
这两行的意思分别是
1、服务端每隔多少秒向客户端发送一个心跳数据
2、客户端多少次没有相应,服务器自动断掉连接
输入以下命令重启ssh配置:
service sshd restart